Contacts of the strand formed by residues 1813 - 1818 (chain D) in PDB entry 1UKJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET1813 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1664D MET* 4.1 21.8 - - + +
1689D TYR* 4.0 24.7 - - + +
1712D TYR* 3.4 15.9 - - + +
1790D HIS 4.5 1.0 - - - +
1791D TYR* 3.4 19.2 - - - -
1792D PRO* 4.9 1.2 - - - +
1810D PRO 5.2 0.9 - - - +
1811D GLY* 3.7 1.2 - - - -
1812D GLY* 1.3 78.4 - - - +
1814D ILE* 1.3 60.1 + - - +
1841D LEU* 3.2 45.3 - - + -
1875D ARG* 3.4 38.6 - - - +
1876D LEU 3.7 10.8 - - - +
1877D SER* 3.5 15.7 - - - -
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Residues in contact with ILE1814 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1664D MET* 4.1 2.9 - - - -
1773D ALA* 3.8 30.5 - - + +
1776D LEU* 4.1 20.9 - - + -
1777D ALA* 4.0 12.8 - - + +
1780D LEU* 4.4 14.8 - - + -
1789D ILE* 4.3 14.4 - - + -
1790D HIS 4.1 7.4 - - - +
1791D TYR* 4.0 16.2 - - + -
1812D GLY 4.7 1.8 - - - +
1813D MET* 1.3 80.3 - - - +
1815D ALA* 1.3 72.4 + - - +
1816D PHE* 4.5 2.9 - - + -
1874D VAL 4.0 0.6 - - - +
1875D ARG* 3.3 4.0 - - - +
1876D LEU* 2.6 51.6 + - + +
1878D VAL* 4.9 4.9 - - + -
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Residues in contact with ALA1815 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1662D PRO 2.9 29.6 - - - +
1664D MET* 3.9 12.1 - - + +
1789D ILE* 3.7 2.3 - - - +
1790D HIS* 2.7 46.0 + - + +
1814D ILE* 1.3 75.7 - - - +
1816D PHE* 1.3 60.1 + - - +
1873D LEU* 4.1 8.1 - - + -
1874D VAL 3.4 7.4 - - - +
1875D ARG* 4.6 7.9 - - + -
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Residues in contact with PHE1816 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1780D LEU* 3.8 23.6 - - + -
1786D VAL* 3.9 20.9 - - + -
1788D LEU 3.2 14.1 - - - +
1789D ILE* 4.0 17.3 - - + +
1790D HIS* 4.2 2.9 + - - -
1814D ILE* 4.5 6.1 - - + -
1815D ALA* 1.3 77.6 - - - +
1817D GLU* 1.3 68.5 + - - +
1818D LEU* 3.9 28.5 - - + -
1828D PHE* 4.1 20.4 - + - -
1872D GLY 3.5 0.5 - - - +
1873D LEU* 3.1 5.5 - - - +
1874D VAL* 2.9 66.1 + - + -
1876D LEU* 3.7 22.9 - - + -
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Residues in contact with GLU1817 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1786D VAL* 3.5 4.0 - - - +
1787D GLU* 2.7 43.9 + - + +
1788D LEU* 2.7 34.8 + - + +
1790D HIS* 3.2 30.3 + - - -
1816D PHE* 1.3 74.5 - - - +
1818D LEU* 1.3 60.3 + - - +
1870D SER* 3.4 35.8 + - - +
1872D GLY 3.2 1.8 - - - +
1873D LEU* 3.7 17.1 - - + +
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Residues in contact with LEU1818 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1785D GLN* 3.4 15.7 - - + +
1786D VAL* 4.5 2.9 - - + -
1787D GLU* 4.6 3.1 - - - +
1816D PHE* 3.9 18.6 - - + -
1817D GLU* 1.3 76.0 - - - +
1819D LYS* 1.3 65.0 + - - +
1820D GLY 4.3 0.2 - - - +
1821D GLY* 3.1 15.6 + - - +
1824D ALA* 3.7 20.2 - - + +
1825D GLY* 3.4 35.9 - - - +
1828D PHE* 4.0 10.1 - - + -
1872D GLY* 2.9 13.6 + - - +
1874D VAL* 4.0 14.6 - - + -
1894D LEU* 3.6 31.2 - - + -
1897D SER* 4.7 5.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il